Liberal Democrat conference organisers have refused a request from the civil liberties campaigner Shami Chakrabarti to address the conference in a debate preceding a crucial vote on secret courts.

The Lib Dems will vote on Tuesday afternoon on the coalition's justice and security bill, which includes proposals to hold more court cases involving sensitive material in secret.

Chakrabarti, the director of Liberty, has been conducting a high-profile campaign against the bill, which she believes will undermine the principles of open justice. She realised the party had the facility to grant outside experts the right to contribute to their debate, and applied for the relevant floor pass on 14 September.

Chakrabarti's application was received by the party's Federal Conference Committee the following day. She was declined two days later, on 17 September.

Faced with motion F41, tabled by the former parliamentary candidate Jo Shaw, which calls for the withdrawal of the whole of part two of the justice and security bill, the party leadership has been increasingly active in lobbying members to back an amendment that would provide wiggle room to strike a compromise on the legislation.

If activists back the motion, against the will of their leadership, it will put pressure on Clegg to return to Westminster and oppose the bill.

The Lib Dems told the Guardian that the biologist Richard Dawkins was granted rights to speak in a debate about science several years ago, as was the former director of Friends of the Earth Jonathan Porritt.

A spokesperson said they had previously declined another application from the actor Hugh Grant to speak about the media and privacy.

Isabella Sankey, director of policy for Liberty, said: "Of course it's disappointing that Liberty's director won't be speaking at the debate but we understand that conference is principally about debate between party members.

"However it's even more disappointing that Lib Dem leadership has tabled an amendment to this principled motion. Rank-and-file Lib Dems understand the importance of open justice and we are confident of their commitment to equality under the law."